Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

Abstract Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memo...

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Bibliographic Details
Main Authors: Guillaume Holley, Páll Melsted
Format: Article
Language:English
Published: BMC 2020-09-01
Series:Genome Biology
Online Access:http://link.springer.com/article/10.1186/s13059-020-02135-8
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spelling doaj-daafcb1da6e540bba1cb2cbe3a969d952020-11-25T03:45:19ZengBMCGenome Biology1474-760X2020-09-0121112010.1186/s13059-020-02135-8Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphsGuillaume Holley0Páll Melsted1Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of IcelandFaculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of IcelandAbstract Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in. Availability https://github.com/pmelsted/bifrosthttp://link.springer.com/article/10.1186/s13059-020-02135-8
collection DOAJ
language English
format Article
sources DOAJ
author Guillaume Holley
Páll Melsted
spellingShingle Guillaume Holley
Páll Melsted
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Genome Biology
author_facet Guillaume Holley
Páll Melsted
author_sort Guillaume Holley
title Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
title_short Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
title_full Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
title_fullStr Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
title_full_unstemmed Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
title_sort bifrost: highly parallel construction and indexing of colored and compacted de bruijn graphs
publisher BMC
series Genome Biology
issn 1474-760X
publishDate 2020-09-01
description Abstract Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in. Availability https://github.com/pmelsted/bifrost
url http://link.springer.com/article/10.1186/s13059-020-02135-8
work_keys_str_mv AT guillaumeholley bifrosthighlyparallelconstructionandindexingofcoloredandcompacteddebruijngraphs
AT pallmelsted bifrosthighlyparallelconstructionandindexingofcoloredandcompacteddebruijngraphs
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